Dear gmx-usersI want to simulate collagen molecule by gromacs. I produce hydroxyprolin parameter by swissparam site: ; ---- ; Built itp for zinc_901791.mol2 ; by user vzoete Mon Jan 12 11:37:34 CET 2015 ; ---- ;
[ atomtypes ] ; name at.num mass charge ptype sigma epsilon CR 6 12.0110 0.0 A 0.387541 0.230120 HCMM 1 1.0079 0.0 A 0.235197 0.092048 CO2M 6 12.0110 0.0 A 0.356359 0.292880 O2CM 8 15.9994 0.0 A 0.302905 0.502080 OR 8 15.9994 0.0 A 0.315378 0.636386 HOR 1 1.0079 0.0 A 0.040001 0.192464 NRP 7 14.0067 0.0 A 0.329632 0.836800 HNRP 1 1.0079 0.0 A 0.040001 0.192464 [ pairtypes ] ; i j func sigma1-4 epsilon1-4 ; THESE ARE 1-4 INTERACTIONS CR CR 1 0.338541 0.041840 CR HCMM 1 0.286869 0.062059 CR CO2M 1 0.347450 0.110698 CR O2CM 1 0.320723 0.144938 CR OR 1 0.326960 0.163176 CR HOR 1 0.189271 0.089737 CR NRP 1 0.334087 0.187114 CR HNRP 1 0.189271 0.089737 [ moleculetype ] ; Name nrexcl zinc_901791 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 CR 1 LIG C1 1 0.0000 12.0110 2 CR 1 LIG C2 2 0.2800 12.0110 3 HCMM 1 LIG H1 3 0.0000 1.0079 4 CR 1 LIG C3 4 0.5030 12.0110 5 CR 1 LIG C4 5 0.3970 12.0110 6 HCMM 1 LIG H2 6 0.0000 1.0079 7 CO2M 1 LIG C5 7 0.9060 12.0110 8 O2CM 1 LIG O1 8 -0.9000 15.9994 9 OR 1 LIG O2 9 -0.6800 15.9994 10 HCMM 1 LIG H3 10 0.0000 1.0079 11 HCMM 1 LIG H4 11 0.0000 1.0079 12 HCMM 1 LIG H5 12 0.0000 1.0079 13 HCMM 1 LIG H6 13 0.0000 1.0079 14 HOR 1 LIG H7 14 0.4000 1.0079 15 NRP 1 LIG N1 15 -0.9060 14.0067 16 HNRP 1 LIG H8 16 0.4500 1.0079 17 HNRP 1 LIG H9 17 0.4500 1.0079 18 O2CM 1 LIG O3 18 -0.9000 15.9994 [ bonds ] ; ai aj fu b0 kb, b0 kb 7 8 1 0.12610 587519.8 0.12610 587519.8 7 18 1 0.12610 587519.8 0.12610 587519.8 1 5 1 0.15080 256422.3 0.15080 256422.3 1 2 1 0.15080 256422.3 0.15080 256422.3 1 10 1 0.10930 287014.9 0.10930 287014.9 1 11 1 0.10930 287014.9 0.10930 287014.9 2 3 1 0.10930 287014.9 0.10930 287014.9 2 4 1 0.15080 256422.3 0.15080 256422.3 2 9 1 0.14180 303937.5 0.14180 303937.5 4 12 1 0.10930 287014.9 0.10930 287014.9 4 13 1 0.10930 287014.9 0.10930 287014.9 4 15 1 0.14800 231490.7 0.14800 231490.7 5 6 1 0.10930 287014.9 0.10930 287014.9 5 7 1 0.15100 230648.0 0.15100 230648.0 5 15 1 0.14800 231490.7 0.14800 231490.7 9 14 1 0.09720 469365.3 0.09720 469365.3 15 16 1 0.10280 371144.2 0.10280 371144.2 15 17 1 0.10280 371144.2 0.10280 371144.2 [ pairs ] ; ai aj fu 1 12 1 1 13 1 1 14 1 1 8 1 1 18 1 1 16 1 1 17 1 2 6 1 2 7 1 2 16 1 2 17 1 3 5 1 3 10 1 3 11 1 3 12 1 3 13 1 3 15 1 3 14 1 4 10 1 4 11 1 4 14 1 4 6 1 4 7 1 5 9 1 5 12 1 5 13 1 6 10 1 6 11 1 6 8 1 6 18 1 6 16 1 6 17 1 7 10 1 7 11 1 7 16 1 7 17 1 8 15 1 9 10 1 9 11 1 9 12 1 9 13 1 9 15 1 10 15 1 11 15 1 12 16 1 12 17 1 13 16 1 13 17 1 15 18 1 [ angles ] ; ai aj ak fu th0 kth ub0 kub th0 2 1 5 1 109.6080 512.48 2 1 10 1 110.5490 383.00 2 1 11 1 110.5490 383.00 5 1 10 1 110.5490 383.00 5 1 11 1 110.5490 383.00 10 1 11 1 108.8360 310.74 1 2 3 1 110.5490 383.00 1 2 4 1 109.6080 512.48 1 2 9 1 108.1330 597.39 3 2 4 1 110.5490 383.00 3 2 9 1 108.5770 470.32 4 2 9 1 108.1330 597.39 2 4 12 1 110.5490 383.00 2 4 13 1 110.5490 383.00 2 4 15 1 106.4930 710.01 12 4 13 1 108.8360 310.74 12 4 15 1 106.2240 525.13 13 4 15 1 106.2240 525.13 1 5 6 1 110.5490 383.00 1 5 7 1 98.4220 198.73 1 5 15 1 106.4930 710.01 6 5 7 1 108.9040 316.16 6 5 15 1 106.2240 525.13 7 5 15 1 112.2380 631.11 5 7 8 1 114.6890 728.07 5 7 18 1 114.6890 728.07 8 7 18 1 130.6000 711.20 2 9 14 1 106.5030 477.55 4 15 5 1 112.2510 519.10 4 15 16 1 111.2060 346.87 4 15 17 1 111.2060 346.87 5 15 16 1 111.2060 346.87 5 15 17 1 111.2060 346.87 16 15 17 1 107.7870 348.08 [ dihedrals ] ; ai aj ak al fu phi0 kphi mult phi0 1 2 4 12 9 0.00 1.3389 1 1 2 4 12 9 180.00 -1.3180 2 1 2 4 12 9 0.00 0.5523 3 1 2 4 13 9 0.00 1.3389 1 1 2 4 13 9 180.00 -1.3180 2 1 2 4 13 9 0.00 0.5523 3 1 2 4 15 9 0.00 -1.3556 1 1 2 4 15 9 180.00 1.1506 2 1 2 4 15 9 0.00 1.2343 3 1 2 9 14 9 180.00 0.5648 2 1 2 9 14 9 0.00 0.4937 3 1 5 7 8 9 180.00 2.6401 2 1 5 7 18 9 180.00 2.6401 2 1 5 15 4 9 0.00 0.5230 3 1 5 15 16 9 0.00 0.3891 3 1 5 15 17 9 0.00 0.3891 3 2 1 5 6 9 0.00 1.3389 1 2 1 5 6 9 180.00 -1.3180 2 2 1 5 6 9 0.00 0.5523 3 2 1 5 7 9 0.00 0.6276 3 2 1 5 15 9 0.00 -1.3556 1 2 1 5 15 9 180.00 1.1506 2 2 1 5 15 9 0.00 1.2343 3 2 4 15 5 9 0.00 0.5230 3 2 4 15 16 9 0.00 0.3891 3 2 4 15 17 9 0.00 0.3891 3 3 2 1 5 9 0.00 1.3389 1 3 2 1 5 9 180.00 -1.3180 2 3 2 1 5 9 0.00 0.5523 3 3 2 1 10 9 0.00 0.5941 1 3 2 1 10 9 180.00 -2.8995 2 3 2 1 10 9 0.00 0.6569 3 3 2 1 11 9 0.00 0.5941 1 3 2 1 11 9 180.00 -2.8995 2 3 2 1 11 9 0.00 0.6569 3 3 2 4 12 9 0.00 0.5941 1 3 2 4 12 9 180.00 -2.8995 2 3 2 4 12 9 0.00 0.6569 3 3 2 4 13 9 0.00 0.5941 1 3 2 4 13 9 180.00 -2.8995 2 3 2 4 13 9 0.00 0.6569 3 3 2 4 15 9 0.00 1.4477 1 3 2 4 15 9 180.00 -1.1088 2 3 2 4 15 9 0.00 0.5816 3 3 2 9 14 9 0.00 1.2468 1 3 2 9 14 9 180.00 -0.5774 2 3 2 9 14 9 0.00 0.7238 3 4 2 1 5 9 0.00 0.2134 1 4 2 1 5 9 180.00 1.4267 2 4 2 1 5 9 0.00 0.6945 3 4 2 1 10 9 0.00 1.3389 1 4 2 1 10 9 180.00 -1.3180 2 4 2 1 10 9 0.00 0.5523 3 4 2 1 11 9 0.00 1.3389 1 4 2 1 11 9 180.00 -1.3180 2 4 2 1 11 9 0.00 0.5523 3 4 2 9 14 9 180.00 0.5648 2 4 2 9 14 9 0.00 0.4937 3 4 15 5 6 9 0.00 0.5146 3 4 15 5 7 9 0.00 0.5230 3 5 1 2 9 9 0.00 -1.4393 1 5 1 2 9 9 180.00 3.6777 2 5 1 2 9 9 0.00 0.9958 3 5 15 4 12 9 0.00 0.5146 3 5 15 4 13 9 0.00 0.5146 3 6 5 1 10 9 0.00 0.5941 1 6 5 1 10 9 180.00 -2.8995 2 6 5 1 10 9 0.00 0.6569 3 6 5 1 11 9 0.00 0.5941 1 6 5 1 11 9 180.00 -2.8995 2 6 5 1 11 9 0.00 0.6569 3 6 5 7 8 9 0.00 -0.2218 3 6 5 7 18 9 0.00 -0.2218 3 6 5 15 16 9 0.00 0.5439 3 6 5 15 17 9 0.00 0.5439 3 7 5 1 10 9 0.00 -0.2929 3 7 5 1 11 9 0.00 -0.2929 3 7 5 15 16 9 0.00 0.5230 3 7 5 15 17 9 0.00 0.5230 3 8 7 5 15 9 180.00 1.2552 2 9 2 1 10 9 0.00 -1.3682 1 9 2 1 10 9 180.00 2.2426 2 9 2 1 10 9 0.00 0.5858 3 9 2 1 11 9 0.00 -1.3682 1 9 2 1 11 9 180.00 2.2426 2 9 2 1 11 9 0.00 0.5858 3 9 2 4 12 9 0.00 -1.3682 1 9 2 4 12 9 180.00 2.2426 2 9 2 4 12 9 0.00 0.5858 3 9 2 4 13 9 0.00 -1.3682 1 9 2 4 13 9 180.00 2.2426 2 9 2 4 13 9 0.00 0.5858 3 9 2 4 15 9 0.00 0.6276 3 10 1 5 15 9 0.00 1.4477 1 10 1 5 15 9 180.00 -1.1088 2 10 1 5 15 9 0.00 0.5816 3 11 1 5 15 9 0.00 1.4477 1 11 1 5 15 9 180.00 -1.1088 2 11 1 5 15 9 0.00 0.5816 3 12 4 15 16 9 0.00 0.5439 3 12 4 15 17 9 0.00 0.5439 3 13 4 15 16 9 0.00 0.5439 3 13 4 15 17 9 0.00 0.5439 3 15 5 7 18 9 180.00 1.2552 2 [ dihedrals ] ; ai aj ak al fu xi0 kxi xi0 kxi 1 2 5 10 2 0.00 0.0000 1 2 5 11 2 0.00 0.0000 2 4 1 9 2 0.00 0.0000 2 4 1 3 2 0.00 0.0000 5 7 1 15 2 0.00 0.0000 5 7 1 6 2 0.00 0.0000 7 8 5 18 2 0.00 107.1941 4 15 2 12 2 0.00 0.0000 4 12 2 13 2 0.00 0.0000 15 4 5 16 2 0.00 0.0000 15 4 5 17 2 0.00 0.0000 #ifdef POSRES_LIGAND [ position_restraints ] ; atom type fx fy fz 1 1 1000 1000 1000 2 1 1000 1000 1000 4 1 1000 1000 1000 5 1 1000 1000 1000 7 1 1000 1000 1000 8 1 1000 1000 1000 9 1 1000 1000 1000 15 1 1000 1000 1000 18 1 1000 1000 1000 #endif I added atomtypes section in .atp file. I added hydroxyprolin hydrogen data in hdb file. I dded [bonds], [angles], [dihedrals] and 2th [dihedrals] in ffbonded.itp file respectively in [ bondtypes ], [ anglestypes ], [dihedraltypes ] and 2th [dihedraltypes ].in the first grompp, this error appeared:number of coordinates in coordinate file (x.pdb, 72323) does not match topology (x.top, 95870) that the difference is equal to sol atom number that is 23547I dont know how can I solve this problem. I appreciate any help. Fatemeh Ramezani -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.